Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.9

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-01-24, 22:24 based on data in: /scratch/project_2003821/RGQMA/RGQMA1


        General Statistics

        Showing 118/118 rows and 9/12 columns.
        Sample Name% mCpG% mCHG% mCHHM C's% Aligned% BP Trimmed% Dups% GCM Seqs
        200022_100_69B_S20_L001_R1_001
        34.8%
        1.0%
        0.5%
        273.2
        44.5%
        0.2%
        88.2%
        33%
        26.5
        200022_100_69B_S20_L002_R1_001
        34.7%
        1.0%
        0.5%
        274.6
        44.5%
        0.2%
        88.3%
        33%
        26.6
        200022_10_B9_B10_S10_L001_R1_001
        38.4%
        0.9%
        0.5%
        1059.6
        48.1%
        0.2%
        91.4%
        33%
        93.4
        200022_11_22B_S11_L001_R1_001
        39.5%
        1.0%
        0.4%
        396.2
        41.4%
        0.2%
        90.4%
        32%
        41.8
        200022_12_27B_S12_L001_R1_001
        36.0%
        0.8%
        0.4%
        420.2
        48.3%
        0.2%
        87.8%
        33%
        35.5
        200022_13_34B_S13_L001_R1_001
        33.8%
        0.8%
        0.4%
        1052.5
        51.1%
        0.2%
        90.7%
        33%
        83.7
        200022_14_38B_S14_L001_R1_001
        35.9%
        0.9%
        0.5%
        482.2
        48.3%
        0.2%
        88.4%
        33%
        41.0
        200022_15_40B_S15_L001_R1_001
        36.8%
        0.9%
        0.4%
        429.3
        45.6%
        0.2%
        89.1%
        33%
        39.4
        200022_16_64B_S16_L001_R1_001
        37.9%
        0.9%
        0.5%
        490.2
        50.4%
        0.2%
        89.0%
        33%
        40.6
        200022_17_67B_S17_L001_R1_001
        33.2%
        0.8%
        0.4%
        529.9
        50.2%
        0.2%
        88.5%
        33%
        43.1
        200022_18_70B_S18_L001_R1_001
        36.7%
        0.9%
        0.4%
        541.8
        46.2%
        0.2%
        89.3%
        33%
        48.6
        200022_19_71B_S19_L001_R1_001
        32.5%
        0.8%
        0.4%
        1147.2
        52.8%
        0.2%
        90.1%
        33%
        86.8
        200022_1_0_B10_S1_L001_R1_001
        34.0%
        0.8%
        0.4%
        453.2
        51.0%
        0.2%
        88.5%
        33%
        37.8
        200022_20_8B_S20_L001_R1_001
        35.5%
        1.0%
        0.6%
        286.6
        41.4%
        0.1%
        90.0%
        36%
        30.1
        200022_21_0_B5_S22_L002_R1_001
        33.7%
        0.8%
        0.4%
        446.7
        50.6%
        0.2%
        85.6%
        33%
        36.5
        200022_22_0_B6_S23_L002_R1_001
        40.5%
        1.0%
        0.4%
        433.2
        43.3%
        0.2%
        87.3%
        32%
        43.8
        200022_23_0_G5_S24_L002_R1_001
        36.5%
        0.8%
        0.4%
        387.4
        52.7%
        0.2%
        83.8%
        33%
        30.1
        200022_24_0_G6_S25_L002_R1_001
        38.8%
        0.9%
        0.4%
        474.7
        46.5%
        0.2%
        86.5%
        33%
        42.5
        200022_25_0_M6_S26_L002_R1_001
        38.1%
        0.9%
        0.4%
        333.1
        43.8%
        0.2%
        85.6%
        33%
        32.4
        200022_26_0_R10_S27_L002_R1_001
        35.5%
        0.9%
        0.4%
        678.7
        50.1%
        0.2%
        86.7%
        33%
        55.5
        200022_27_0_R2_S28_L002_R1_001
        37.2%
        0.8%
        0.4%
        377.8
        52.5%
        0.2%
        84.4%
        33%
        30.1
        200022_28_0_R3_S29_L002_R1_001
        33.7%
        0.8%
        0.4%
        751.8
        55.3%
        0.2%
        86.4%
        33%
        55.3
        200022_29_G4_0_S30_L002_R1_001
        36.9%
        0.9%
        0.4%
        448.9
        47.8%
        0.2%
        85.9%
        33%
        39.6
        200022_2_0_B2_S2_L001_R1_001
        38.3%
        0.9%
        0.4%
        316.9
        49.2%
        0.2%
        87.3%
        33%
        27.8
        200022_30_G6_0_S31_L002_R1_001
        39.0%
        0.8%
        0.4%
        888.1
        46.7%
        0.2%
        89.6%
        33%
        79.1
        200022_31_12B_S32_L002_R1_001
        37.3%
        0.9%
        0.4%
        794.4
        48.0%
        0.2%
        89.4%
        33%
        70.2
        200022_32_21B_S33_L002_R1_001
        35.1%
        0.8%
        0.4%
        499.2
        51.2%
        0.2%
        85.3%
        33%
        39.8
        200022_33_31B_S34_L002_R1_001
        33.5%
        0.8%
        0.4%
        359.6
        48.8%
        0.2%
        84.0%
        33%
        30.0
        200022_34_32B_S35_L002_R1_001
        35.2%
        0.8%
        0.4%
        430.8
        48.1%
        0.2%
        86.2%
        33%
        37.3
        200022_35_39B_S36_L002_R1_001
        37.4%
        0.9%
        0.4%
        393.3
        41.7%
        0.2%
        87.8%
        32%
        40.3
        200022_36_48B_S37_L002_R1_001
        28.3%
        0.7%
        0.4%
        1492.5
        59.9%
        0.1%
        85.5%
        33%
        95.8
        200022_37_50B_S38_L002_R1_001
        38.2%
        0.9%
        0.4%
        319.5
        46.7%
        0.2%
        85.1%
        33%
        29.7
        200022_38_54B_S39_L002_R1_001
        36.9%
        0.9%
        0.4%
        382.7
        49.1%
        0.2%
        85.4%
        32%
        33.5
        200022_39_59B_S40_L002_R1_001
        36.9%
        0.8%
        0.4%
        476.9
        51.4%
        0.2%
        85.3%
        33%
        39.4
        200022_3_0_B3_S3_L001_R1_001
        39.9%
        0.9%
        0.4%
        352.1
        42.3%
        0.2%
        89.8%
        33%
        35.9
        200022_40_73B_S41_L002_R1_001
        35.0%
        0.8%
        0.4%
        406.0
        50.0%
        0.2%
        84.9%
        33%
        33.6
        200022_41_0_B8_S1_L001_R1_001
        37.3%
        1.0%
        0.5%
        477.1
        46.9%
        0.3%
        91.7%
        32%
        43.0
        200022_42_0_G1_S2_L001_R1_001
        34.9%
        0.9%
        0.5%
        378.8
        48.9%
        0.2%
        89.5%
        32%
        31.6
        200022_43_0_M3_S3_L001_R1_001
        36.8%
        1.0%
        0.5%
        437.0
        49.8%
        0.2%
        91.0%
        33%
        36.9
        200022_44_0_M7_S4_L001_R1_001
        38.5%
        1.0%
        0.6%
        654.9
        45.8%
        0.2%
        93.2%
        32%
        61.0
        200022_45_0_R4_S5_L001_R1_001
        35.7%
        1.0%
        0.5%
        508.8
        46.0%
        0.2%
        91.6%
        32%
        45.8
        200022_46_0_R6_S6_L001_R1_001
        34.6%
        0.9%
        0.5%
        410.3
        50.7%
        0.2%
        89.9%
        32%
        32.9
        200022_47_B5_0_S7_L001_R1_001
        33.4%
        1.0%
        0.5%
        399.2
        48.3%
        0.2%
        89.5%
        33%
        33.8
        200022_48_B9_0_S8_L001_R1_001
        36.0%
        1.1%
        0.6%
        394.8
        43.7%
        0.2%
        90.9%
        32%
        38.3
        200022_49_G8_0_S9_L001_R1_001
        36.0%
        1.0%
        0.5%
        503.6
        46.8%
        0.2%
        91.7%
        33%
        45.1
        200022_4_0_B4_S4_L001_R1_001
        39.9%
        0.9%
        0.4%
        356.0
        43.8%
        0.2%
        89.1%
        33%
        34.5
        200022_50_R1_R2_S10_L001_R1_001
        35.2%
        1.0%
        0.5%
        368.7
        43.4%
        0.2%
        91.0%
        32%
        36.3
        200022_51_14B_S11_L001_R1_001
        34.7%
        1.0%
        0.5%
        831.8
        50.6%
        0.2%
        92.9%
        32%
        69.4
        200022_52_18B_S12_L001_R1_001
        33.6%
        0.9%
        0.5%
        427.7
        54.9%
        0.2%
        88.9%
        33%
        31.6
        200022_53_26B_S13_L001_R1_001
        33.7%
        0.9%
        0.5%
        420.6
        48.5%
        0.2%
        89.9%
        32%
        35.9
        200022_54_28B_S14_L001_R1_001
        36.3%
        1.0%
        0.5%
        500.2
        46.8%
        0.2%
        91.9%
        33%
        45.2
        200022_55_29B_S15_L001_R1_001
        36.8%
        1.0%
        0.6%
        386.5
        43.7%
        0.2%
        91.6%
        32%
        38.3
        200022_56_47B_S16_L001_R1_001
        37.3%
        1.0%
        0.5%
        365.9
        43.8%
        0.3%
        91.8%
        32%
        36.0
        200022_57_49B_S17_L001_R1_001
        33.7%
        1.0%
        0.5%
        616.4
        46.5%
        0.2%
        93.0%
        33%
        56.8
        200022_58_52B_S18_L001_R1_001
        34.6%
        1.0%
        0.5%
        461.0
        45.9%
        0.2%
        91.3%
        32%
        42.3
        200022_59_62B_S19_L001_R1_001
        34.8%
        1.0%
        0.5%
        430.9
        47.5%
        0.2%
        91.2%
        33%
        39.0
        200022_5_0_G4_S5_L001_R1_001
        36.7%
        0.8%
        0.4%
        422.1
        50.1%
        0.2%
        87.7%
        33%
        34.3
        200022_60_74B_S20_L001_R1_001
        34.5%
        1.0%
        0.5%
        454.7
        44.9%
        0.2%
        91.3%
        32%
        43.9
        200022_61_0_G9_S22_L002_R1_001
        38.0%
        1.0%
        0.5%
        317.0
        41.9%
        0.3%
        91.1%
        33%
        33.8
        200022_62_0_M4_S23_L002_R1_001
        38.3%
        1.0%
        0.5%
        408.0
        43.9%
        0.2%
        90.9%
        33%
        41.5
        200022_63_0_M8_S24_L002_R1_001
        38.6%
        1.0%
        0.5%
        603.8
        41.4%
        0.2%
        93.8%
        33%
        64.6
        200022_64_0_M9_S25_L002_R1_001
        35.3%
        0.9%
        0.5%
        613.5
        47.8%
        0.2%
        92.2%
        33%
        55.6
        200022_65_0_R7_S26_L002_R1_001
        36.7%
        1.1%
        0.5%
        349.5
        41.7%
        0.3%
        91.0%
        32%
        36.9
        200022_66_0_R8_S27_L002_R1_001
        39.3%
        1.1%
        0.5%
        398.2
        39.6%
        0.3%
        91.8%
        32%
        45.8
        200022_67_G1_0_S28_L002_R1_001
        39.4%
        1.1%
        0.5%
        292.6
        42.1%
        0.2%
        90.5%
        33%
        31.1
        200022_68_G2_0_S29_L002_R1_001
        39.3%
        1.1%
        0.5%
        367.2
        40.5%
        0.2%
        91.3%
        32%
        40.8
        200022_69_G3_G4_S30_L002_R1_001
        38.3%
        1.0%
        0.5%
        287.3
        45.3%
        0.2%
        89.7%
        33%
        28.1
        200022_6_0_M10_S6_L001_R1_001
        40.2%
        1.0%
        0.4%
        337.5
        41.5%
        0.2%
        89.7%
        32%
        35.5
        200022_70_R3_R4_S31_L002_R1_001
        38.5%
        1.0%
        0.5%
        522.7
        47.8%
        0.2%
        91.8%
        33%
        47.6
        200022_71_10B_S32_L002_R1_001
        36.8%
        1.1%
        0.6%
        689.1
        43.6%
        0.2%
        93.4%
        33%
        70.0
        200022_72_13B_S33_L002_R1_001
        34.1%
        1.0%
        0.6%
        395.8
        50.1%
        0.2%
        88.6%
        33%
        33.5
        200022_73_24B_S34_L002_R1_001
        37.6%
        1.1%
        0.6%
        397.7
        47.5%
        0.2%
        89.2%
        33%
        36.7
        200022_74_30B_S35_L002_R1_001
        31.3%
        0.9%
        0.5%
        450.3
        54.5%
        0.2%
        88.6%
        34%
        33.9
        200022_75_35B_S36_L002_R1_001
        37.6%
        1.0%
        0.5%
        374.6
        45.7%
        0.2%
        90.2%
        33%
        35.1
        200022_76_61B_S37_L002_R1_001
        38.1%
        1.0%
        0.6%
        348.0
        47.1%
        0.2%
        90.1%
        34%
        31.7
        200022_77_63B_S38_L002_R1_001
        37.9%
        1.0%
        0.5%
        945.9
        43.1%
        0.3%
        94.2%
        32%
        98.1
        200022_78_65B_S39_L002_R1_001
        36.5%
        1.0%
        0.5%
        426.4
        44.5%
        0.2%
        90.9%
        33%
        42.1
        200022_79_68B_S40_L002_R1_001
        36.8%
        1.0%
        0.5%
        387.2
        48.5%
        0.2%
        90.6%
        33%
        34.6
        200022_7_0_M2_S7_L001_R1_001
        39.7%
        0.9%
        0.4%
        355.9
        46.2%
        0.2%
        88.5%
        33%
        32.6
        200022_80_72B_S41_L002_R1_001
        37.1%
        1.0%
        0.5%
        328.4
        43.3%
        0.2%
        90.3%
        32%
        33.1
        200022_81_B1_0_S1_L001_R1_001
        39.8%
        1.1%
        0.6%
        198.7
        43.5%
        0.2%
        87.8%
        33%
        20.1
        200022_81_B1_0_S1_L002_R1_001
        39.7%
        1.1%
        0.6%
        200.2
        43.5%
        0.2%
        87.8%
        33%
        20.3
        200022_82_B2_0_S2_L001_R1_001
        40.1%
        1.1%
        0.6%
        183.0
        41.1%
        0.3%
        86.8%
        33%
        19.5
        200022_82_B2_0_S2_L002_R1_001
        40.1%
        1.1%
        0.6%
        183.8
        41.1%
        0.3%
        86.9%
        33%
        19.5
        200022_83_B3_0_S3_L001_R1_001
        36.8%
        0.9%
        0.5%
        211.6
        47.0%
        0.2%
        80.1%
        32%
        20.4
        200022_83_B3_0_S3_L002_R1_001
        36.8%
        0.9%
        0.5%
        212.2
        47.0%
        0.2%
        80.3%
        32%
        20.4
        200022_84_B6_0_S4_L001_R1_001
        38.8%
        1.1%
        0.6%
        201.0
        42.3%
        0.3%
        87.4%
        33%
        20.9
        200022_84_B6_0_S4_L002_R1_001
        38.7%
        1.1%
        0.6%
        202.2
        42.3%
        0.3%
        87.4%
        33%
        21.0
        200022_85_B7_B8_S5_L001_R1_001
        44.7%
        1.2%
        0.6%
        198.8
        38.2%
        0.3%
        89.1%
        32%
        23.2
        200022_85_B7_B8_S5_L002_R1_001
        44.7%
        1.2%
        0.6%
        199.8
        38.2%
        0.3%
        89.2%
        32%
        23.3
        200022_86_G1_G2_S6_L002_R1_001
        37.7%
        1.0%
        0.5%
        217.3
        42.3%
        0.2%
        88.1%
        33%
        22.2
        200022_87_G9_G10_S7_L001_R1_001
        35.2%
        1.0%
        0.5%
        227.3
        46.5%
        0.2%
        86.2%
        33%
        21.1
        200022_88_M1_M2_S8_L001_R1_001
        38.9%
        1.0%
        0.5%
        219.9
        42.8%
        0.3%
        88.1%
        33%
        22.4
        200022_88_M1_M2_S8_L002_R1_001
        38.8%
        1.0%
        0.5%
        221.3
        42.8%
        0.3%
        88.2%
        33%
        22.5
        200022_89_M9_M10_S9_L001_R1_001
        39.3%
        1.0%
        0.6%
        234.5
        45.2%
        0.2%
        87.5%
        33%
        22.5
        200022_89_M9_M10_S9_L002_R1_001
        39.3%
        1.0%
        0.6%
        235.7
        45.2%
        0.2%
        87.7%
        33%
        22.6
        200022_8_0_M5_S8_L001_R1_001
        37.6%
        0.9%
        0.5%
        577.8
        49.0%
        0.2%
        89.4%
        33%
        49.5
        200022_90_R9_R10_S10_L001_R1_001
        37.5%
        1.1%
        0.5%
        196.6
        42.0%
        0.3%
        86.5%
        33%
        20.5
        200022_90_R9_R10_S10_L002_R1_001
        37.5%
        1.1%
        0.5%
        197.2
        42.0%
        0.3%
        86.6%
        33%
        20.6
        200022_91_33B_S11_L001_R1_001
        40.2%
        1.1%
        0.5%
        208.0
        40.4%
        0.3%
        88.0%
        32%
        22.7
        200022_91_33B_S11_L002_R1_001
        40.2%
        1.1%
        0.5%
        209.0
        40.4%
        0.3%
        88.1%
        32%
        22.8
        200022_92_37B_S12_L001_R1_001
        35.6%
        1.0%
        0.5%
        234.6
        43.4%
        0.2%
        87.7%
        33%
        23.6
        200022_92_37B_S12_L002_R1_001
        35.5%
        1.0%
        0.6%
        235.7
        43.3%
        0.2%
        87.8%
        33%
        23.7
        200022_93_3B_S13_L001_R1_001
        38.4%
        1.0%
        0.5%
        214.8
        41.6%
        0.3%
        87.8%
        32%
        23.0
        200022_93_3B_S13_L002_R1_001
        38.4%
        1.0%
        0.5%
        215.4
        41.6%
        0.3%
        88.1%
        33%
        23.1
        200022_94_41B_S14_L001_R1_001
        34.8%
        1.0%
        0.6%
        202.6
        43.7%
        0.2%
        88.1%
        34%
        20.2
        200022_94_41B_S14_L002_R1_001
        34.7%
        1.0%
        0.6%
        204.2
        43.7%
        0.2%
        88.3%
        34%
        20.3
        200022_95_45B_S15_L001_R1_001
        34.6%
        0.9%
        0.5%
        246.9
        47.3%
        0.2%
        87.1%
        33%
        22.5
        200022_95_45B_S15_L002_R1_001
        34.5%
        0.9%
        0.5%
        248.3
        47.3%
        0.2%
        87.1%
        33%
        22.6
        200022_96_4B_S16_L001_R1_001
        33.8%
        0.9%
        0.5%
        261.4
        48.2%
        0.2%
        87.7%
        33%
        23.5
        200022_96_4B_S16_L002_R1_001
        33.7%
        0.9%
        0.5%
        263.4
        48.2%
        0.2%
        87.7%
        33%
        23.7
        200022_97_51B_S17_L001_R1_001
        35.3%
        1.0%
        0.5%
        258.5
        44.7%
        0.2%
        88.0%
        33%
        25.2
        200022_97_51B_S17_L002_R1_001
        35.3%
        1.0%
        0.5%
        260.1
        44.7%
        0.2%
        88.0%
        33%
        25.3
        200022_98_58B_S18_L001_R1_001
        36.0%
        1.0%
        0.5%
        262.7
        43.3%
        0.2%
        88.4%
        33%
        26.3
        200022_98_58B_S18_L002_R1_001
        36.0%
        1.0%
        0.5%
        264.7
        43.3%
        0.2%
        88.4%
        33%
        26.5
        200022_99_5B_S19_L001_R1_001
        36.8%
        1.0%
        0.5%
        229.2
        40.8%
        0.3%
        88.8%
        32%
        24.7
        200022_99_5B_S19_L002_R1_001
        36.7%
        1.0%
        0.5%
        229.7
        40.9%
        0.3%
        88.8%
        32%
        24.7
        200022_9_B8_0_S9_L001_R1_001
        32.8%
        0.8%
        0.4%
        411.1
        54.6%
        0.2%
        86.6%
        33%
        30.4

        Bismark

        Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

        Alignment Rates

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Strand Alignment

        All samples were run with --directional mode; alignments to complementary strands (CTOT, CTOB) were ignored.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cytosine Methylation

        loading..

        M-Bias

        This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Trimmed Sequence Lengths

        This plot shows the number of reads with certain lengths of adapter trimmed.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..